srtsim_cci_ref {SRTsim}

Generate Data with Cell-Cell Interaction Under Reference-Based Mode

Description

Generate Data with Cell-Cell Interaction Under Reference-Based Mode

Usage

srtsim_cci_ref(
  EstParam = NULL,
  numGene = 1000,
  location_in,
  region_cell_map,
  fc = 3,
  LR_in,
  sim_seed = 1,
  numKNN = 4,
  numSingleCellType = 2000
)

Arguments

EstParam

A list of estimated parameters from srtsim_fit function, EstParam slot if the simSRT object.

numGene

An integer specifying the number of genes in the synthetic data, default is 1000

location_in

A dataframe with x, y, and region_label

region_cell_map

A dataframe specifying the cell type proportion in each region. Row: region,Column: cell type.

fc

A number specifying effect size for ligand-receptor pairs that mediate the cel-cell communication, default is 3

LR_in

A dataframe specifying ligand and receptor pairs, containing four columns: protein_a, protein_b, celltypeA, and celltype B

sim_seed

A number for reproducible purpose

numKNN

A number specifying number of nearest neighbors with elevated gene expressin levels, default is 4

numSingleCellType

A number specifying number of spots in the background pool. Gene expression count are then sampled from this background pool.

Value

Returns a SRTsim object with a newly generated count matrix and correspoding parameters